


#8: Hydra

by Winchester_Writer



Series: 10 Times Tony Stark Saved Peter Parker and 2 Times He Couldn't [8]
Category: Marvel Cinematic Universe
Genre: Other, Talks and explanations of torture
Language: English
Status: Completed
Published: 2019-08-14
Updated: 2019-08-14
Packaged: 2020-08-23 10:21:05
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 3,079
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/20241259
Author URL: https://archiveofourown.org/users/Winchester_Writer/pseuds/Winchester_Writer
Summary: Peter gets taken by Hydra





	#8: Hydra

**Author's Note:**

> This story has graphic depictions of hurting and torture. If this is triggering please do not read this. 
> 
> I'm sorry in advance for the pain....

Spider-Man was becoming more and more of a hero and Peter would always smile at that thought. Tony Stark, however, was not so happy about it. He knew that the more popular Peter became, the more threats he would have. Peter had already been poisoned once and Tony almost lost him then, he couldn’t go through that again. That’s why Tony was constantly updating the Spider-suits and trying to make them impervious to pretty much everything. 

It was a Monday morning and Tony was sitting in a really, really boring meeting. His phone buzzed in his pocket and he looked at it. The text was from Underoos. 

“ **Heading there earlier from school, Mr. Stark. Something feels off, almost feels like I’m being followed.”**

Tony immediately panicked a bit, but then told himself to breathe. He stood up and started to walk out of the meeting, one of the men asking him where he was going. 

“Sorry, as much as I’d love to stay, there’s a more pressing matter to deal with. Avengers business.”

He strolled out of the room and hopped into the elevator, texting Peter back.

“ **It’ll be okay, Underoos. I’m up in the lab, meet me there.” **

Peter was walking through the cold Manhattan streets and he couldn’t shake the feeling that someone was following him. His Spider-senses were tingling and standing up constantly, he couldn’t make it stop. He picked up the pace and made it to Stark Tower in record timing. He breathed a sigh of relief as he stepped into the elevator, heading straight up to the lab. 

“Hey, Mr. Stark!” he yelled as he walked into the lab. 

“Hey, Underoos. How are you?”

“I’m okay,” Peter said and grabbed a granola bar and an apple from the little snack bowl that Tony had set out by the entrance. 

“What were you talking about? The feeling like someone was watching you?”

“Oh y’h,” his mouth was full of food. 

“Pete,”

He swallowed and then talked. 

“Sorry, Mr. Stark. I was walking from school to here and I just couldn’t shake the feeling that someone was watching me. It was like they were just following me as I walked here. I know it sounds stupid, but my Spider-Senses were acting up and I couldn’t get rid of it. I know, Mr. Stark, it’s stupid. It’s probably nothing.”  
“You’re right, it’s probably nothing, but it isn’t stupid. I get those feelings sometimes too. Most of the time you just have to brush them off and keep on going. I think it’s a side effect of the whole superhero gig, sometimes you get these uneasy feelings.”

“Okay, Mr. Stark. I’m sorry for being so irrational about this.”

“You’re not being, Pete. Now, I have something exciting I want to show you.”

“Okay.” 

Tony started walking towards the other side of the lab and Peter realized that there was another door there, that wasn’t there on Friday when he came. 

“Mr. Stark, why is there a new door?”

“You’re about to find out, Underoos.”

Tony grabbed the door handle and opened it up. He smiled as Peter’s mouth dropped open and he gasped. 

“Welcome to your very own new room, Pete.”

Peter didn’t say anything, he just walked into the room and looked around. The was a giant Queen size bed in the middle of the room. It had blue sheets and a tiny Iron Man stuffed toy in the middle, which Peter chuckled at. To the left side was a night table with a lamp and alarm clock. On the other side was a nice wooden desk with multiple shelves and drawers. The last thing in the room made Peter’s mouth drop even more. Straight across from the bed was a giant flat screen TV with a full on gaming center. Peter finally got his voice back. 

“Mr. Stark, is this all for me?”

“Yeah it is, kid. I talked to your Aunt May and she thought it would be good for you if you could hang out at the lab a little bit more. So I decided that if you were going to hang out here and spend the night then you’d need a place to stay. It’s all yours, Underoos.”

Peter ran and latched onto Tony, hugging him furiously. 

“Thank you, thank you, thank you!”

“Alright kid, that’s enough. You’re welcome Underoos.” 

Peter let go and then looked around the room again. He took his backpack and put it on the desk, well his desk actually. 

“I’ll let ya get settled and then you can come back to the lab. May thought it would be good for you to stay overnight on the weekends when you come for Friday lab days.”

“Thank you so much Mr. Stark!”

“Yeah, yeah, Underoos.”

Tony walked out and then Peter walked out about 30 minutes late, a look of awe still on his face. The two worked on some new thrusters for his suit for a while and then it was finally time for Peter to head home. It was such a good day, the perfect day, according to Peter. He said thank you to Tony again and then walked home. 

Peter, however, never made it home that day. He was walking through the back-alleys, knowing that it was faster than the normal route. He was tired and cold, but he was still really excited about the room. He thought about bringing in some posters and pictures to make it feel a little more homey. He was so wrapped up in his thoughts that he didn’t hear the swift footsteps approaching him from behind. 

A hand covered his mouth and Peter immediately started fighting back. He was thrashing and kicking, fighting with all of his strength against whoever had grabbed him. All of the sudden, he felt a sharp pain in his leg and then he was drifting off into blackness. 

Something felt off to Tony, like something was wrong. He couldn’t place it, but something just felt wrong. He finally placed the feeling, it was about Underoos. He decided to call May, she picked up after two rings. 

“Tony, is something wrong?”

“No, no. Everything is fine May. How are you?”

“I’m good, enjoying my night of peace. I’m guessing that Peter decided to stay over in his new room. He hasn’t come home so I’m assuming he’s there.”

“Oh yeah! He loves it. The kid couldn’t stop thanking me.”

“Well, do you remember when you got him a new back-pack and he thanked you like 20 times? You just got him a brand new room, it’s gonna be more than that.”

“Yeah, I guess it is. Well, it was nice talking to you, May. I’m gonna go check on Underoos, see if he wants to have a movie night.”

“Night, Tony. Thank you for everything.”

Tony’s heart was beating in his chest, his breathing was becoming a little erratic. Where the heck was Underoos? He started blowing up his phone, over and over again. Finally there was an answer. 

“Ah, Tony Stark. We were expecting a call from you.”

That wasn’t Underoos.

“Who are you? What have you done with my kid?”

“I think you know who we are. Cut off one head and two more shall take its place. Don’t worry about your precious Peter Parker. We’re taking great care of him.”

The phone got pointed towards Peter and Tony could hear him screaming. 

“Let him go you son of a,”

The line went dead. Tony was freaking out, but he had enough sense to ask Karen to track the phone. The Hydra agents had blocked the tracking device and it would take a solid 24 hours for Karen to successfully hack and track Peter’s phone. Tony was officially having a panic attack. His kid was gone and was being tortured by some sadistic Hydra doctor. This was a time when he needed backup, so he made a call. He hadn’t even thought about the flip phone since Steve had sent it to him, but now it was all he could think about. He fumbled through his desk and finally found it. He dialed Steve as quickly as possible. 

“Tony?” came the groggy and gruff voice.

“Steve, I don’t care what happened at the airport, I don’t care about anything that happened between us. My kid is in trouble and I need to get him back. I need your help on this one.”

“Your kid? What are you talking about Tony?”

“I’ll explain when you get here, just please get here, Steve, please.”

“I’ll be there by tomorrow morning, Tony.”

He hung up and sunk down onto the ground, not breathing properly. He stayed that way for a long time, until the sun was starting to come up. He had told Steve to meet him in the training room. Tony stood up, brushed himself off and then walked down to the training room, taking a deep breath as he saw Steve and the rest of the team walk in. 

Peter was in pain, so much pain. He was strapped down to some sort of chair in some sort of facility. Soldiers were walking in and out and there were men in lab coats that kept coming and injecting him with things. The liquid made it feel like his entire body was on fire and he couldn’t get it to stop. He was thrashing and screaming, begging Mr. Stark to come and rescue him. Finally, the serum or whatever they were injecting him with was wearing off. The man in the lab coat walked over to him and smiled. 

“Ahh, you’re awake, good. Now the fun can really begin. We shall see what this spider is made of.” 

There was a cutting sensation and then pain like fire shot through his side. Peter screamed so loud that the entire building heard him. After the cutting came the actual fire, the burning on his side and on his arms. He bit down so hard that he tasted blood in his mouth. He was going to die, he was sure of it. 

Tony had just finished explaining everything to Steve and the rest of the team.

“So, let me get this straight. Peter is Spider-Man, the one you recruited to fight us in the parking lot. After that, you took him under your wing and have been mentoring him. He became like your son and now he’s been kidnapped by Hydra.”

“Exactly. I kept calling him and finally Hydra answered. Karen is currently trying to track his phone. We should be able to find him in about 5 hours.” 

“Alright, until then we wait and then we’ll go and find him.”

Tony nodded his head and then Steve asked for the rest of the Avengers to leave the room. Tony had taken a seat and then Steve approached him, putting a hand on his shoulder. 

“Tony, everything that happened, I’m sorry, I really am. I know what it feels like to lose someone so important to you, that’s the way I felt with Buck.”

“Yeah. I’m sorry too Capsicle. I understand now, the way you were feeling about getting Bucky back. You’d tear down Heaven and Hell if it meant getting them back. I’m sorry I didn’t understand that until now. We good now, Cap?”

“Yeah, Tony, we’re good.”

“Great, now no more mushy stuff. I need to get my kid back.”

Steve gave a head nod and then joined the rest of the team, preparing them for whatever they were going to meet. 

Peter was being cut into, lit on fire, beat, and chopped up. The doctor kept experimenting, figuring how much it would take until the Spider broke. He moved onto the worst of the worst. 

The doctor chuckled, “you don’t need your appendix do you, Spider?”

The knife cut into Peter’s side and he screamed bloody murder. He could feel the blade cutting through every layer of skin. All of a sudden he felt a tugging sensation and then his appendix was ripped out. He screamed so loud that he felt his vocal chords tear ever so slightly. 

The doctor just laughed. 

“Mr. Stark, we have coordinates for Peter Parker.”

“Send them to my suit, Karen. Avengers, suit up!”  
The group was already ready to go, but Tony didn’t realize that. He was too focused on Peter. The team lined up and entered one of the QuinJets, coordinates set for Peter’s location. He hoped that his kid was still breathing. 

The Hydra building was small and Underground, no match for the entire Avengers team. Peter was being held in a small room on the outskirts of the building. When they stormed in, the Avengers all split up, going in different directions. Natasha took the outskirts of the building and was the first one to find Peter.   
“I found him,” she whispered into the com. 

She could barely talk. Peter was strapped down to a bed. Dried blood and fresh blood covering practically every inch of him. He had burn marks all over his body and he was writhing in pain. 

Tony yelled that he was on his way and Natasha quickly told him no.

“Why not?!”   


“You don’t want to see him like this, Tony.”

Natasha grabbed the straps and ripped them off of Peter. He started shaking and crying. 

“Come on my, little spider, open up your eyes for me, please.”

Peter’s eyes fluttered open, “‘sha”

“Yeah, hi Peter. It’s me, it’s Natasha. I’m here. We are all here. Tony is outside taking care of the mean Hydra men. I’m gonna carry you out of here, okay.”

“‘Sha”

“Yep, I’m here.”

He started to cry and sputter, basically gurgling at Natasha.  
“Shh, Pauchok, I’m here, Aunt Natasha is here.”

Natasha carefully picked Peter up and carried him out of the building, laying him down on the bed in the QuinJet. The rest of the Avengers came in a little bit later. Tony was frantic, he ran into the Jet, immediately screaming for Peter. 

“Where is he, Nat?”

“He’s on the bed in the medical area.”

Tony brushed past Natasha even though she was protesting and immediately he stopped dead in his tracks. Peter looked like he was dead. There was blood all over him, injury marks littered every part of his body.

“Underoos?”

Peter didn’t respond. Crap, he wasn’t responsive, he wasn’t moving. 

“CLINT, GET THIS THING FLYING!”

The group made it back to Stark Tower in record timing. Tony scooped up Peter and ran with him to the med-bay. They got him into a hospital-bed and rolled him into emergency surgery. Peter wasn’t going to wake up for a couple of days and Tony was refusing to leave his side. He was sitting in a chair right next to Pete’s bed in the ICU. Finally, after 3 days Natasha came in and forced Tony to get up and go get some proper food and a shower. Tony didn’t argue, you don’t argue with Black Widow. 

Tony left and within 10 minutes, Peter was waking up, lolling his head from side to side. 

“Tasha.”

“Hey Petey, I’m here.”

“What happened?”

“You got taken by some not nice people, Pete. We came and saved you, but they did some damage before we got to you.”

“Oh. H’rts.”

“Yeah, I’m afraid it’s going to for a while, Pauchok.”

“Huh?”

“Oh, it’s a Russian nickname, Petey. It means Little Spider.”

“Oh. M’ter S’rk?”

“He just went to grab some food and a shower. He’ll be back soon, I promise.”

“Ok.”

Peter reached out for Natasha and she grabbed his hand, letting him latch on. He was scared, she could tell. Scared, but at least he was safe. The two stayed like that until Tony came into the room. 

“Underoos?”

“M’ter S’rk.”

“Hey Pete, how are you?”

Natasha slipped out of the room and let the two have some privacy. 

“H’rts”

“I know Pete, I know. It will for a little bit. You have some pretty bad injuries, but you’ll be okay. “

“Saved me.”

“Yeah Underoos, I did. The Team and I came and saved you.”

“Team?”  
“Yeah, I called in the Avengers, Pete. We needed the team to save you.”

“Oh.”

“You rest now, Pete, you need to regain your strength.”

As soon as Peter fell asleep, Tony let the tears fall. He was relieved that Pete was okay, but he was also scared to death. His kid had been taken and hurt, almost killed. He felt like he had failed. Finally, he pulled himself together, convincing himself that he had to be strong for Underoos. 

Two weeks later and Peter was feeling well enough to leave the med-bay. The doctor had come in and cleared him, so Peter was anxious to get out. Tony helped him walk through Stark Tower and into the lounge. The rest of the Avengers were there waiting for him. Natasha immediately walked up to him and kissed his forehead. 

“I’m glad you’re safe, my little spider.”

“Thank you for saving me, Aunt Natasha.”

“No need to thank me, little one.”

He continued walking and was greeted by the rest of the Avengers. 

“Hey I’m Clint.”

Peter shook his hand, “thank you for saving me.”

“No problem.”

Peter stared in awe as he came face to face with Captain America. Mr. Stark had called Captain America, but they weren’t on speaking terms? 

“Hi Peter. I’m Steve. Tony has told me a lot about you.”

“Um,” he shook Cap’s hand, “it’s nice to meet you Mr. Captain America Sir.”

Steve chuckled, “Steve is fine, kid.”

“Oh um okay, Steve.”

“You’re strong, kid. You said you’re from Queens?”

“Yes, Sir.”

“You got heart and strength kid. I’m glad Tony choose you.”

“Uh, thank you.”

Tony interrupted, “Alright Pete, you need to go and lay down. You can in your

room and binge watch science documentaries or something.”

“Okay, dad.”

He walked out of the lounge, waving goodbye to everyone. Clint and Steve were shocked. 

“Did he just call you dad?” Clint asked. 

“Yeah, he did.”

“But he isn’t your actual son,” Steve gaped. 

“Yeah, no kidding Sherlock. He isn’t my son, but I’m the closest thing he’s ever had to a dad.”

“It’s true,” Natasha continued, “and to be honest, they make a really good father/son duo.”

“We do, don’t we?” Tony asked, smiling. 

His kid was back at home, safe in his new room and new bed. Everything was going to be okay. 

  
  
  
  
  


**Author's Note:**

> Thank you so much for reading. I hope you don't hate me too much. Any comments and kudos would be appreciated!


End file.
